Environmentally persistent free radicals (EPFRs) have been widely detected in polycyclic aromatic hydrocarbon (PAH)-contaminated soils, but the activation of persulfate by inherent EPFRs in PAH-contaminated soil for the transformation of PAHs remains unclear. In the present study, benzo[a]pyrene (B[a]P) was selected as a representative PAH and its transformation in a persulfate/B[a]P-contaminated soil system was studied without the addition of any other activator. Results indicated that EPFRs in the soil activated persulfate to produce reactive oxygen species (ROS) and degraded B[a]P. It was found that the decomposition of persulfate was accompanied with the decay of EPFRs in the soil, which was quantified using electron paramagnetic resonance (EPR) technique. Correspondingly, combined with EPR and quenching experiments, it was confirmed that sulfate radicals (SO4˙-), hydroxyl radicals (˙OH), superoxide radicals (˙O2-) and singlet oxygen (1O2) coexist in the reaction system, and ˙O2- and 1O2 play major roles in the degradation of B[a]P. Primary intermediates were identified via gas chromatography-mass spectrometry (GC-MS), and the transformation pathway underlying B[a]P degradation was proposed. Furthermore, the acute and chronic toxicities of seven intermediates to aquatic organisms were predicted using Ecological Structure Activity Relationships (ECOSAR) software, and the corresponding results showed that the seven intermediates detected were very toxic to the environment. This study provides new insights into the activation of persulfate by EPFRs in the degradation of refractory pollutants.